Although I understand and agree with the above statement, it is VERY dealer dependent. My 2013 F-150 Ecoboost had down pipes, exhaust, intake, hot and cold side piping, intercooler and custom tuning. One of the coolant lines to the turbo started leaking and the dealer changed it without issue, all the while staring at the stainless downpipes which were inches away. The wrong dealer would have denied the warranty claim. Its a crap shoot.It may cause future warranty issues if the dealership documents that the car has a custom tune.
With that said, removing custom tuning is not a bad idea prior to dealer service. That way they can flash any updates without issue.